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RNA as building blocks


Tormod

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I posted a story from Purdue News today, here:

http://www.hypography.com/article.cfm?id=34269

 

Here is the abstract for the story:

 

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Bottom-up assembly of RNA Arrays and Superstructures

as Potential Parts in Nanotechnology

 

Dan Shu, Wulf-Dieter Moll, Zhaoxiang Deng,

Chengde Mao and Peixuan Guo

(Department and Pathobiology and Department of Chemistry)

 

DNA has been extensively scrutinized for its feasibility as parts in nanotechnology, but another natural building block, RNA, has been largely ignored. RNA can be manipulated to form versatile shapes, thus providing an element of adaptability to DNA nanotechnology, which is predominantly based upon a double-helical structure. The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging pRNAs (pRNA), which together form a hexameric ring via loop/loop interaction. Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and arrays several microns in size via interaction of programmed helical regions and loops. RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

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I was wondering if this kind of thing has any impact on the recent discussions we've had on RNA being the building blocks of life.

 

Would this imply that these nanotech machines are living entities?

 

TeleMad, I would be especially interested in your comments on this story.

 

Tormod

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Gotta run off to work right now so can't get into to it much. But one question first. In OOL studies, a type of RNA called pRNA is sometimes investigated. But there, pRNA stands for pyranosyl RNA, which is a non-biological six-membered ring version of RNA (instead of the biological five-membered - furanosyl - ring). Is that the type of pRNA being discussed, or does pRNA stand for "packaging RNA" in the context of the abstract you posted?

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Boy, I feel like an infant. How little I know about the chemical processes of RNA. I hope this discussion delves further into it.

 

As to nano-tech as a living entity/ life form. Especially based on emulation of RNA. First I do not think we consider RNA a living entity/ life form in and of itself. So I do not see where that would help catagorize something as a living entity.

 

Nor am I aware of any advances in nano-tech regarding AI, self MOTIVATED reproduction. Does pre=programmed mechanical self reproduction define a living entity?

 

(Edit to correct at least one typo)

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And even the "organic" vs "inorganic" thing. Organic merely means it is carbon based. Thus if the nano-device was carbon based construction it WOULD be organic. Confusing things even more.

 

Maybe "life" is determined by whether there is some not for profit org started to defend it's continued existence? :-)

 

One of the great things about being involved in this site is what you learn when chasing down answers for here. Almost unsuprisingly, there is actually a web site CALLED

 

What is Life?

 

"Intended for the Advancement of Public Understanding of the Biological Sciences

 

What is Life presents conceptual thinking in biology. While many current issues in biology are based on simple ideas, the elucidation of biological mechanisms that explain diverse aspects of life is challenging because cells and organisms are complex systems. To understand how biologists study the structure and function of living organisms one has to understand the relationship between experiment and theory. Such an understanding amounts to scientific literacy. "

 

http://www.whatislife.com/index.html

 

The home page is a portal to many great aricles and resources on the topic.

 

One I enjoyed browsing was:

 

"Man and Machine

 

Man and machine has fascinated mankind for a long time. Making man more like a machine and a machine like man are irresistible goals for many people. 20th Century technology, computers, and genetics have brought us closer to this goal. Computer simulations of life forms, artificial intelligence, robotics are all testimony to these efforts."

 

http://www.whatislife.com/news/news_artificiallife.html

 

This site might not provide a hard line defintion, but it sure helps expand the dialog!

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Ah, I read the abstract again and am pretty sure that the pRNA mentioned is not the non-biological pyranosyl RNA, because it comes from a bacteriophage...

 

The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging pRNAs (pRNA), which together form a hexameric ring via loop/loop interaction.

 

So it must be some kind of packaging RNA.

 

I am somewhat familiar with viral packaging processes in general. For example, in the lamba virus, a concatomer is a long tandem repeat of viral genomes produced by the host cell, with the copies of the genome being separated by COS sites (nucleotide sequences where proteins will bind). After empty viral heads are produced, the concatomer is processed: proteins bind at the COS sites and package the intervening viral genome into a prefabricated empty viral head: then the tail is attached to produce a complete virion. I guess the phage mentioned in the abstract uses a completely RNA - or a combination protein-RNA - 'machine' to package its genome.

 

Now that I have a better idea what they are discussing, I'll see what I think as far as OOL is concerned.

 

 

 

Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and arrays several microns in size via interaction of programmed helical regions and loops. RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

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Abstract: DNA has been extensively scrutinized for its feasibility as parts in nanotechnology, but another natural building block, RNA, has been largely ignored.

 

As far as OOL is concerned, RNA (ribonucleic acid) is less stable that DNA (deoxyribonucleic acid). RNA has a reactive hydroxyl group (-OH) on C2’ while DNA has only a hydrogen atom (hence, the 2’ carbon of DNA has been “deoxy’d”, making it deoxyribonucleic acid). As one example, RNA is not stable in alkaline conditions that DNA is quite “comfortable” in. So even if RNA does turn out to better than DNA in nanotechnology, that doesn’t necessarily – and most likely doesn’t - carry over into OOL.

 

Abstract: RNA can be manipulated to form versatile shapes, thus providing an element of adaptability to DNA nanotechnology, which is predominantly based upon a double-helical structure.

 

Yes, cellular DNA is rather a bland character as far as conformation is concerned: it exists as a double helix consisting of two anti-parallel polynucleotide chains that spiral around a common axis. There is very little conformational variation (DNA in cells is typically a right-handed double helix, called the B form. Sometimes other forms – such as A or even Z – can exist in cells, but even then, there really isn’t too much range of shape for cellular DNA. If one adds DNA-binding proteins, then the DNA double helix can be bent and otherwise “distorted”, but that requires proteins in addition to DNA).

 

Cellular RNA, on the other hand, comes in several shapes. mRNA is basically a single-stranded, linear polyribonucleotide; tRNA adopts an L shape (a “clover leaf” when considering only a two-dimensional view); and rRNA adopts a kind of globular 3-D shape…something like. RNA can forms loops, stem-loops, pseudoknots, and other complex shapes – these can lead to catalytic capabilities. Catalytic RNAs are called ribozymes (but technically, not all ribozyme are catalysts).

 

So even in cells one can see a fairly wide range of shapes and functions for RNA, including catalytic abilities. Now, since RNA can carry genetic information, and, can also perform catalytic functions, OOL researchers figure it’s the perfect solution to the chicken-or-egg paradox associated with the origin of the interrelated and interdependent associations between DNA, RNA, and proteins in extant cells.

 

So RNA is definitely a good target for OOL research, whether this article has anything to say on the matter or not.

 

Abstract: The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging pRNAs (pRNA), which together form a hexameric ring via loop/loop interaction. Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and arrays several microns in size via interaction of programmed helical regions and loops. RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence.

 

Maybe that’s relevant…maybe it’s not. Without these “triangles” and other shapes, RNA has been shown capable of partial replicase activity. I have little to no doubt that RNA molecules can be created that can replicate themselves – the question is, how likely is it that those replicases could arise spontaneously? As an analogy, we know that silicon and other elements can be made into a Pentium 4 CPU, but we don’t expect that such would occur spontaneously.

 

Abstract: Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

 

Which might be a negative in regards to OOL: depends on exactly what they mean. For example, if the RNA arrays are unusually stable because they are very rigid, then their catalytic capabilities would likely be reduced relative to more flexible molecules

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  • 1 year later...
___I stumbled on this geometric view of DNA RNA structure; the main idea revolves on mappings on a sphere's surface.

http://www.codefun.com/

http://www.codefun.com/Geometry.htm

 

___I don't know enough chemistry to say it's relevant or not, but it has the bright twinkling light of geometry that draws me in every time. :)

Cool link Turtle, I sent them straight to my favorites.
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I think I'm missing something but I thought RNA is the factory within which globular and structural protein 'shapes' are produced. If someone wanted to build molecular machines, they'd resequence DNA (the recipe), let RNA at it (the chef) to produce proteins (the Beef Wellington).

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